2023 Projects

Translation of the genetic code into protein is an essential and highly regulated cellular process. Translation initiation is the rate limiting step of this process, and translational misregulation is linked to a number of diseases. Eukaryotic translation initiation factors (eIFs) are essential to translation initiation. eIF3 is involved in every core event of translation initiation and is responsible for the formation of a pre-initiation complex (PIC), an assembly of eIFs and tRNA on the 40S ribosomal subunit, which binds mRNA and initiates protein expression. However, the mechanistic functions of specificeIF3 subunits, including those in the mRNA-entry-channel-arm, remain unknown. We are employing two different approaches to investigate the function of these subunits, which will allow us to understand how mutations in eIF3 contribute to aberrant translation. We use a reconstituted system which incorporates the key players of translation initiation and tracks its core events, including mRNA recruitment, PIC formation, and binding of eIF3 to the PIC, usinga gel shift assay. We aim to explore the interactions of variants of the 40S subunit and eIF3 using this system and quantitatively compare it with binding of wild-type 40S and eIF3 to give us mechanistic insight into the function of eIF3. Concurrently, we are conducting proteomic analysis on eIF3 variants to understand the effects of mutations that mimic the loss of the mRNA-entry-channel arm and the loss of the whole complex. Previous ribosome profiling results identified mRNAs whose expression was most changed by these eIF3 mutations. We are comparing these results to TMT-mass spectrometry results, which quantifies the proteins present in the cell, to analyze how mutations to eIF3 affect protein expression. Both our in vivo and in vitro approaches will help us understand the contributions of each eIF3 subunit in translation initiation and how mutations in eIF3 and the ribosome impact translation.

Translation is the process by which mRNAs are recruited and read by ribosomes to synthesize proteins within cells. Translation initiation, the first and most highly regulated step of translation, begins with several eukaryotic initiation factors (eIFs) and tRNA assembling to form a pre-initiation complex (PIC) that attaches to the small ribosomal subunit. Attachment of the PIC allows for mRNA recruitment and location of the mRNA sequence that starts protein assembly. eIF3 is the largest, most complex eIF and is essential for formation of the PIC. To better understand eIF3’s role in translational regulation, we are investigating the Degron mutant of eIF3, which results in complete loss of eIF3 function. Previous ribosome profiling experiments used wild-type and Degron strains to determine several mRNA transcripts whose translation efficiency was most significantly changed with the loss of eIF3 function. However, these experiments were time consuming and difficult to complete in an undergraduate lab setting. We are testing an alternative approach involving polysome profiling and long read sequencing, which achieves the same goals as ribosome profiling while streamlining the workflow and eliminating extraneous data. We use polysome profiling to separate mRNA attached to multiple ribosomes (polysomes) from mRNAs with fewer ribosomes attached. We then purify total RNA and polysome RNA for use in long read sequencing, enabling us to detect structural variants of RNA that we would be unable to capture using other sequencing methods. We believe utilizing long read sequencing will allow for more accurate identification and quantification of translational differences between wild-type and Degron mutant eIF3 strains, giving us additional insight into the mechanism of eIF3.

Translation is an essential process in all cells that involves ribosomes binding to messenger RNA (mRNA), recognizing

the start codon(AUG), and reading gene-coding sequences to assemble proteins. Translation initiation is a highly regulated pathway that starts with forming the pre-initiation complex (PIC), which involves numerous eukaryotic initiation factors (eIFs) loading onto the small ribosomal (40S) subunit. The PIC first binds at the 5’ end of mRNA and scans through the 5’-un-translated region (5’-UTR) until locating the start codon. When the PIC’s mRNA entry channel arm is open, it allows for mRNA binding and scanning. Upon start-codon recognition, the arm closes and stops scanning. eIF3 is the largest factor participating in the pathway and is required for mRNA recruitment. In yeastS. cerevisiae, 5 major subunits of eIF3 contribute to each core event during translation initiation, including mRNA recruitment to the PIC. We explore the DDKK mutation in S. cerevisiae, which impairs the entry channel arm. We used prior ribosome profiling data to identify mRNAs whose translation is known to relatively increase or decrease in the presence of the DDKK mutation. However, it is unclear if translational efficiency can be attributed to 5’-UTRs. To investigate the role of 5’-UTRs inmRNA’s sensitivity to DDKK we introduce plasmids with the sensitive5’-UTR, the corresponding gene’s first 20 codons, and Firefly Luciferase. The PIC has to scan through the 5’- UTR before the ribosome translates Luciferase, so the amount of Luciferase expression corresponds with how efficiently translation occurs. Since Luciferase is expressed as light, we can measure luminescence levels of the DDKK and wildtype (WT) cells. By comparing Luciferase expression in DDKK and WTcells we can dissect the effect of 5’-UTRs and first 20 codons on mRNA sensitivity to the DDKK mutation.

The human microbiome – a culmination of bacteria, viruses, and other microorganisms that live in and on our bodies – has been heavily studied in recent years. Studies have found strong evidence linking the interactions between our cells and these organisms with the regulation of numerous systems within the human body. It is also believed that dysbiosis, or an imbalance of the microbiome, can contribute to inflammatory responses and the progression of certain diseases. Myalgic Encephalomyelitis, or Chronic Fatigue Syndrome (ME/CFS), is a multisystem disease that is characterized by debilitating fatigue, post-exertional malaise, and cognitive impairment. Patients present with a wide variety of symptoms, with many left bedridden and unable to complete normal daily tasks. There is currently no known cause or cure for ME/CFS, but recent studies indicate that a disturbance in the gut microbiome may be linked to the development of the condition. To investigate this, we collected fecal samples from ME/CFS patients and healthy controls to study the presence and relative abundance of bacterial species. Using gene sequencing and microbiome analysis technology, I observed that the samples from ME/CFS patients presented with decreased microbiome diversity and a disproportionate dominance of certain bacterial cultures compared to controls. Additionally, I observed that within ME/CFS patients, there was a further decrease in microbiome diversity in those with gastrointestinal symptoms, such as nausea or IBS. I concluded that our ME/CFS patients had noticeable changes in the composition of their gut bacteria, supporting the idea that the symptoms of ME/CFS are linked to dysbiosis of the gut microbiome. Further investigation into this phenomenon will allow us to better understand ME/CFS and how to treat it.

Myalgic encephalomyelitis (ME/CFS), commonly known as chronic fatigue syndrome, is a complex and debilitating diso der with no known cure. Common symptoms such as post-exertional malaise, unrefreshing sleep, impaired daily function, cognitive impairment, and gastrointestinal symptoms make it difficult for patients to live comfortably. Many factors such as genetic predisposition, microbiome dysbiosis, and previous infection all have a role to play in causing the dysregulated immune system seen in patients with ME. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that regulates gut mucosal and neuro-inflammation and influences gut permeability by microbially derived AhR agonists such as tryptophan metabolites. We hypothesize that a deficiency in tryptophan metabolites in people with ME/CFS leads to the increased inflammation and gut permeability seen in patients with the disease.I investigated the optimal incubation time and concentration to detect AhR-induced gene expression using a known AhR ligand. To do this,I cultured human Caco-2 cells, made cDNA, and used qPCR to measure expression of genes of interest and housekeeping gene GAPDH. I found the optimal incubation time for the AHRR gene, 6 hour incubation with a 2.5uM FicZ concentration and serum free media. Using these conditions, I tested expression of AHRR with stool samples of patients with ME/CFS and healthy controls. There is no difference in expression of AHRR between patients of ME/CFS and healthy controls, and further experimentation is necessary to determine AHR’s role in ME/CFS pathophysiology.

Recent studies have shed light on the complex and dynamic communities of gut microbes and their effects on the various bodily systems, including the immune, nervous, and endocrine systems. Alterations in the gut microbiome, known as dysbiosis, as well as changes in gut permeability, contribute to inflammation. Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS), is an incurable multi-system disease characterized by persistent fatigue, sleep problems, post-exertional malaise, and cognitive impairment. Dysbiosis may play a role in ME/ CFS, acting as both a symptom and a cause of disease, contributing to inflammation and disease progression. The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that regulates gut mucosal membranes and neuro-inflammation while also influencing gut permeability by micr bially derived AhR agonists such as tryptophan metabolites.

Studies have shown that these AhR ligands moderate disease severity. The effect of AhR activation is model- and ligand-spe- cific, yielding either pro- or anti-inflammatory responses. In conjunction, dysbiosis and gastrointestinal symptoms present in ME/CFS suggest that AhR dysregulation may contribute to ME/CFS pathophysiology. Thus, we hypothesized that the gut microbiomes of people with ME/CFS are deficient in the pro- duction of AhR agonists by tryptophan, amplifying gut permea- bility and pro-inflammatory responses. To test this, I measured the capacity of stool cultures to induce AhR-regulated gene expression. Using DNA amplification technology, I observed that AhR-related gene fold expression did not vary significantly between ME and control samples. However, ME patients with cognitive symptoms returned an almost significant value, warranting future investigation. Furthermore, we know that our experiment induces AhR-related gene expression, meaning that we should examine other genes of interest to see if they elucidate different results.

Currently, many of the genes inDrosophila melanogaster remain uncharacterized, especially genes involved in regulating metabolism. This summer, we focused on characterizing the CG5577 gene. Sequence similarity suggests this gene encodes a likely member of the haloacid dehydrogenase (HAD) domain superfamily of non-protein phosphatases, in particular, a protein similar to human pyridoxal phosphate phosphatase (PDXP). One function of PDXP is to dephosphorylate pyridoxal 5’-phosphate (PLP), the co-enzymatically active form of vitamin B6. Vitamin B6 is a crucial nutrient that maintains not only our muscular and skeletal structure but also our cognitive abilities. Our goal for this project is to determine if the CG5577 gene is the possible ortholog to PDXP by knocking out the CG5577 gene in Drosophila and determining if our mutants show similar phenotypes as reported in previous studies in other species. These phenotypes in mutant mice include muscle degeneration, neurodegeneration, and improper locomotion behavior. So far, we have seen that our mutants have decreased flight performance compared to our controls, as well as increased sensitivity to longer exposure times to carbon dioxide. Mutant females also have possible fertility defects. These results tell us this gene possibly affects muscle function and other aspects of physiology. Understanding more about how Drosophilaregulates vitamin B6 levels may give us a better understanding of how it is regulated in humans. This can help develop treatments for diseases where vitamin B6 is unregulated, such as epilepsy, depression, certain cancers, and other neurological disorders.

Insects are the most diverse group of animals on Earth, with over 1 million described species and an estimated total of over 20 million in total. Insects play a vital role in ecosystems, as pollinators, predators, and decomposers. They are also a major source of food for many other animals. However, insect populations are threatened in many regions, and habitat loss due to human activities is among the most prescient threats to insect biodiversity. Managed wild spaces can be a valuable tool in preserving insect populations. The Preserve at Vassar is a 525-acre multi-use space situated south of Vassar College campus, consisting of farmland, wildflower grasslands, deciduous forests, wetlands, streams, and riparian buffers. The preserve is located within the borders of the city of Poughkeepsie, NY, a developed urban area, acting as a wildlife refuge. In this study, we measured insect family diversity, evenness, and abundance across forests and grasslands using sweep netting and pitfall traps to collect a variety of plant and soil-dwelling insects, respectively. We then compared these metrics between forest sites and grassland sites to determine geographical differences between insect family composition and diversity.

Orb-weaving spiders catch almost every kind of flying insect, except one: moths. Spiders in the sub-family Cyrtarachninae are moth-specialists, and they appear to do so, in part, by making an aggregate glue that is very different from that of other orb-weaving spiders. This difference in composition, we hypothesize, allows for a rapid drying of the moth specialist glue as it spreads into moth wings, gluing down scales before they are able to be shed and the prey escapes. Given the importance of this glue in capturing moths, we sought to understand the biochemical properties of moth-specialist aggregate glue droplets and compare them to typical orb-weavers. To understand how these glue droplets vary in their spreading ability and chemical distribution, we used Raman Spectroscopy to analyze the spatial distribution of the chemical components of glue droplets that were allowed to spread on calcium fluoride surfaces. We analyzed the moth-specialist species Cyrtarachne ixoides andCladomelea akermani, and three generalist species Trichonephila clavipes, Gasteracantha cancriformis, and Argiope argentata. For all species except C. akermani, we analyzed four locations: droplet core, capture thread interface with the dro let, intermediate space within the droplet, and the edge of the droplet. For C. ixoides, we observed an additional structure of tendrils within the droplet and also took measurements there. Because Cladomelea akermani’s web consists of only a single droplet at the end of a thread and only three locations were tested: the intermediate space, the coiled windlass and the droplet edge. SpectraGryph was used to compare silk and pure amino acid spectra to identify composition in each locationof Cyrtarachne yunoharuensis. We hypothesize that in spread glue droplets there exists gradients of each chemical constituent, whether they are moth-specialist or generalist. This research is supported by the National Science Foundation, project #2031962 to CD and JL

With the worsening of climate change in recent decades, invasive species have been able to proliferate and threaten ecosystems worldwide. Without intervention, this could lead to the loss of natural environments which provide invaluable ecosystem services. Ampelopsisbrevipedunculata, commonly known as Porcelain berry, is a temperate liana native to Asia which has begun to dominate ecosystems in the northeastern United States. The control of invasive plants such as this one is a multifaceted problem requiring a breadth of knowledge in order to inform possible management options. This project aims to investigate the photosynthetic characteristics and overall physiology of the vine in order to better understand how the plants become established under different light conditions in order to inform management and restoration efforts. Specifically, A. brevipedunculata exhibits two varying leaf morphologies: lobed leaves and heart shaped leaves. Why these two morphologies appear and how their photosynthetic characteristics vary is at the heart of this research project. Characteristics of leaves from both morphotypes were analyzed under sun and shade

conditions in order to determine photosynthetic characteristics relating to light use, carbon dioxide use, and chlorophyll fluorescence, as well as anatomical differences. Preliminary results indicate that lobed leaves exhibit increased thickness and chlorophyll levels, and have higher photosynthetic rates than their heart-shaped counterparts in both sun and shade conditions. This has the potential to inform future management efforts to most effectively reduce invasive vine populations.

TiO2 is commonly used asa semiconductor material in dye-sensitized solar cells(DSSCs), photovoltaic cells in which molecular dyes are paired with an inorganic semiconductor to convert solar energy into electrical power. Molecular dyes are often bound to semiconducting nanoparticles using chemical substituents that serve as anchoring groups adsorbed on the surface of the metal oxide. Historically, carboxylic acid has been used as an anchor group in DSSCs, but new anchor groups are currently being explored, such as boric acid, which has exhibited improved power conversion efficiency. In this study, density functional theory was used to calculate the adsorption energies of boric acid and functionalized boronic acids on the rutile TiO2 (110) surface to identify potential candidates for use as anchor groups. Adsorption configurations, including molecular and dissociative configurations, were constructed on two differently sized slab models and then optimized using DFT+U-D3. DFT+U-D3 was also used to calculate the electronic and vibrational energies. We identified 4-fluorophenyl boronic acid in a bidentate dissociative configuration as the most stable binding configuration on the rutile TiO2 (110) surface.

Anchoring groups facilitate covalent bonding between the photo sensitive dye and the semiconductor in dye-sensitized solar cells. We have introduced boric acid as a new anchoring group on a TiO2 rutile (110) surface, as it may exhibit stronger adsorption than the more commonly used formic acid and phosphonic acid. Previous studies examined boric acid adsorption on a clean TiO2 surface, but in this study, the surface is hydrated

to represent a more realistic model of adsorption. We created five models of the hydrated TiO2 rutile (110)surface, placing dissociated water in the form of OH- and H+ on Ti5c and Ob binding sites, respectively, near the boronic acid adsorption site. Multiple configurations of boric acid adsorption were then examined. DFT+U-D3 was used to optimize the structures and calculate the adsorption energy for each configuration. The doubly dissociated bidentate configuration was the most stable, which is consistent with previous work. Boric acid adsorption is less stable on a hydrated surface than on a clean surface in all of the configurations considered.

Tau is an intrinsically denatured protein that stabilizes and supports the microtubules in neuronal axons. Despite its intrinsically denatured form, Tau has the ability to self-asso- ciate into fibers and neurofibrillary tangles, the development of which has been linked to neurodegenerative diseases like Alzheimer’s Disease. Thus, a greater understanding of tau’s isoforms and their behaviors is required. The Donhauser Lab aims to characterize the morphology and behavior of different isoforms of tau using atomic force microscopy. Afterpolym- erizing Tau isoforms to form fibers, topographical images of the fibers are captured. Currently, the lab relies on human eyes to identify fibers in AFM images; however, such subjective identification leads to faulty characterization and inconsistent measurements. The aim of the current project was to develop an image analysis routine that automatically identifies the positions, lengths, and branching patterns of Tau fibers in AFM images. This automated routine will eliminate the inaccuracies and imprecisions of human analysis. Using the image analysis toolbox in MatLab, binarization, skeletonization, and branch point identification were used to create a consolidated program that automatically analyzes an AFM image. With this program, the lab can now bridge the gap between a qualitative AFM image and quick, accurate quantitative analysis of tau fibers.

Tau is a neuronal protein best known for its role in microtubule stabilization and organization. In its pathogenic state, however, tau forms filamentous, insoluble aggregates called paired helical filaments (PHFs) that have been found within Alzheimer’s disease-affected neurons. However, the details surrounding tau’s role in neurodegenerative disease pathology remain unclear. This project studies the mechanical properties of tau that may affect its neurotoxicity. Tau’s unstructured nature has allowed it to elude traditional protein structural characterization methods such as crystallography, but analysis with atomic force microscopy (AFM) offers a novel method to interrogate tau structure. We hope to characterize the nature of the polyelectrolyte brush that surrounds the fiber core of tau aggregates. Investigating the behaviors of this brush, composed of the protein’s unstructured termini, can provide insight into which mechanical properties contribute to tau aggregation and will ultimately deepen our understanding of the protein’s role in the progression of neurodegenerative disease. Thus far, a protocol has been developed that has allowed us to capture high-resolution images of tau assemblies. Going forward, this protocol will be used to observe the deformation and adhesion of the polyelectrolyte brush surrounding tau PHFs.

The microtubule associated protein tau has six naturally occurring isoforms formed through alternative splicing. The ratios of the  seisoforms differ at different stages of development as well as in association with different neurodegenerative diseases. One major way in which isoforms differis by the presence or absence of two N terminal inserts in the projection domain. This region of the proteinis characterized by a high number of negatively charged amino acids at physiological pH and is implicated with the formation of a polyelectrolyte brush that applies an electrostatic force which could help with the organization of microtubules in neurons. This project aims to evaluate the physical properties of the 0n4r,1n4r, and 2n4r tau isoforms using atomic force microscopy (AFM) to learn more about the impact of the N terminal inserts on the physical properties of tau. To do this, tau is incubated on a mica substrate and an AFM tip and forces are measured between the two tau layers. So far, this project has confirmed that in all the studied isoforms the projection domain extends from the surface into a polyelectrolyte brush and that the force from the brush likely does vary with the presence of the N terminal inserts, with more inserts likely contributing to a longer-range force. Going forward, there will be more work on standardizing the force measurements as well as applying other techniques towards evaluating the differences between isoforms.

Tau, a microtubule-associated protein, plays a crucial role in neuronal functions such as microtubule stabilization and regulation in axons. Abnormal variants, mutations, and post-translational modifications of tau are linked to neurodegenerative diseases, in which tau aggregates into structures called paired helical filaments. Our work focuses on the projection domain of tau, a region of the protein that may have an impact on its propensity for aggregation. Atomic force microscopy (AFM) force curves help us understand tau’s structure based on its intramolecular force interaction with the microscope tip as the tauis binded to a mica substrate. Achieving reproducibility in these force curves is challenging due to the variability in the size of conventional sharp AFM tips. To address this, in the current work we have employed larger colloidal AFM probes in an attempt to obtain more consistent data. This method may reduce variability, as the larger probe averages the force over a larger surface area, making it less sensitive to local surface differences. Our lab has collected some preliminary data as we develop the best possible method for using colloidal probes. We eventually expect or hope to obtain a wider and consistent set of force curves for 2N4R wild-typetau so that eventually, this method can be used to characterize and, thus, compare its force curves to other variants.

Tau is an intrinsically disordered protein responsible for the regulation and stabilization of microtubules in neuronal axons. However, tau can aggregate into neurofibrillary tangles, a precursor to neurodegenerative disease. It is thus important to understand fully the protein’s relevant structures and physical behaviors. The atomic force microscope (AFM) is used to study tau’s structure, including the protein’s disordered domains, which are difficult to study with traditional protein structure characterization tools. Previous work has shown that when tau is deposited onto a surface of mica and the AFM probe tip, it adopts a configuration similar to when it binds to microtubules, and projects its N-terminal to form polyelectrolyte brushes. In this geometry, the forces exerted by the projection domains interacting between the two layers can be measured. In the current study, a novel method is developed in which tau is absorbed on only the mica surface to determine if reproducibility of these types of measurements can be improved. The method aims to maintain the cleanliness of the AFM’s tip in accordance with previous work. This has produced promising results in terms of reproducibility, as it allows for less repulsive force from tau when the tip is lowered and more uniform forces between the tip and tau layers.

In our pursuit of a novel tandem reaction involving an epox- ide-opening/ Friedel-Crafts reaction in order to realize the shortest-to-date total synthesis of the natural product Brazilin, we discovered two new unexpected reaction modes of 2,3-ep- oxy alcohols which occurred on two different model systems. With the model system derived from 1-indanone, a 5-membered ring model system, we have identified a high-yielding, 4-step synthetic route to 2-naphthols mediated by trifluoroacetic acid while using no chromatographic purification until the final step. This reaction is the result of an intermolecular rearrangement followed by aromatization, which results in significant structural change under very mild reaction conditions. Using the model system derived from -tetralone, a 6-membered ring model system, we have identified a novel C-C bond fragmentation. Also mediated by trifluoroacetic acid, this fragmentation results in a significant structural change and the formation of two new carbonyl functional groups. Both of these discoveries are extremely synthetically useful in their own way and are thus far unprecedented. Given the operational simplicity and exceptionally mild reaction conditions, both reactions are currently being optimized and their scope is being expanded upon.

Daphynepapytone A is a sesquiterpenoid natural product that is found in stem extracts of Daphne papyracea. First isolated in 2021, Daphnepapytone A showed inhibitory activities against -glycosidase, signifying potential uses for treating type 2 diabetes. The complex carbon skeleton is comprised of a four-membered ring within a six-membered ring within a seven-membered ring. This project aims to synthesize Daphnepapytone A in the laboratory through two photochemical reactions involving a bicyclic dienonere arrangement and an intramolecular [2+2] cycloaddition. As the compound has not been synthesized previously, existing literature methods for individual reactions were combined to produce a synthesis route. Two model systems, where the starting materials were pared down to simpler compounds, were developed to streamline the overall scheme to determine if the proposed synthetic route was feasible. Both model systems are in progress, and one has reached the first key photochemical reaction. The present priority is to improve the efficacy of each synthetic step through replication, altering the reagent combinations, and varied procedures to optimize the reaction yields on the model systems. Each model system addresses different components of the final tetracyclic compound in order to have a twofold validation of the proposed synthesis route. Once the key reactions have been demonstrated on the model systems, the synthetic route will be applied to synthesize Daphnepapytone A using the appropriate starting materials. By making Daphnepaptyone A in the laboratory, other compounds within the Daphnepapytone family can be synthesized using related methods.

Antibiotic resistance poses a significant public health concern, as the increased spread can lead to untreatable infections, rendering current antibiotics ineffective. Antibiotic Resistant Genes (ARGs) are often encoded on small, circular pieces of DNA called plasmids which are primarily shared in bacterial populations through conjugative plasmid transfer (CPT). Research on the molecular basis of CPT is lacking, and greater understanding may help us create new therapeutics. pSK41 is the founding member of the largest family of plasmids from gram positive bacteria Staphylococcus aureus. MRSA, methicil lin resistant S. aureus, is considered a serious level threat by the Centers for Disease Control (CDC) with over 10,000 deaths per year. Methicillin resistance, along with others, are carried on plasmids in the pSK41 family, thus understanding CPT of these plasmids is crucial. DuringC PT, a multiprotein complex, called the relaxosome, processes the plasmid for transfer. CPT starts at the origin o ftransfer (oriT), a conserved DNA sequence on the plasmid. Genes adjacent to the oriT typically code for the components of the relaxosome. Here we characterize pSK41 orf62, a small protein encoded near the pSK41 oriT. We performed an expression test and successfully overexpressed orf62 in BL213 DE3 Gold cell line. Orf62 was then purified using nickel affinity and size exclusion chromatography. Circular dichroism demonstrated that orf62 was mostly beta sheets and coils, which aligned with the predicted structural model generated with AlphaFold. Future experiments include optimized purification, crystallography, and an Electrophoretic Mobility Shift Assay (EMSA) to verify binding to the oriT.

20a StructuralCharacterization of Conjugative Proteins from pCU1 and pSK41

Jordan Norman, ’24and Professor Krystle McLaughlin

Increased antibiotic resistance in bacteria decreases the efficacy of existing antibiotics, posing a significant financial and public health concern. The spread of antibiotic resistant genes between bacteria occurs primarily through the process of conjugative plasmid transfer, or CPT. In addition to carrying antibiotic resistant genes, many of the proteins involved in CPT are also encoded directly on the plasmid. This includes the relaxosome, a protein complex that processes plasmid DNA for transfer, as well as factors that regulate the transcription of plasmid-derived proteins. pCU1 is a plasmid isolated  from Salmonella Typhimurium and pSK41 is a plasmid isolated from Staphylococcus aureus. Here, we present studies to characterize TraK, TraI, and Orf90. TraK is an accessory protein from the pCU1 relaxosome, TraI is a relaxase/helicase from the pCU1 relaxosome, and Orf90 is a transcription factor from pSK41.

To examine TraK, TraI, and Orf90, each protein was overexpressed in Escherichia coli BL21(DE3), extracted, and purified using affinity chromatography and size exclusion chromatography. This methodology yielded pure TraK, TraI, and Orf90. For TraKand Orf90, the structure of the purified proteins was then examined using circular dichroism.

Circular dichroism results showed that the secondary structure of TraK is 57.9 % alpha helical and 34.2% percent disordered.

The results revealed that the secondary structure of Orf90 is 7.5%alpha helical, 31.6% beta sheet, and 45.5% disordered. Additionally, TraK was imaged using atomic force microsco py to determine its volume and shape. Future experiments include examining interactions between TraK and TraI using isothermal titration calorimetry and atomic force microscopy. Additionally, we plan to do DNA footprinting with Orf90 to determine the specific DNA sequence to which it binds. We hope these studies will provide further insight into CPT and, ultimately, prevent the spread of antibiotic resistance in bacteria

Bacteroides thetaiotaomicron (B. theta), a gram-negative bacteria in the human gut microbiome, is one of the primary organisms responsible for the digestion of complex polysaccharides. It does so through the use of polysaccharide utilization loci (PUL). These co-regulated regions of DNA encode proteins that participate in polysaccharide degradation and transport. Studying the PUL system and its mechanisms can improve understanding of gut health. This research focuses on the structural characterization of and interaction between two components of PUL: TonB-dependent transporters (TBDT) and anti-sigma factors. TBDTs are transmembrane proteins that are highly specific and only operate in the presence of certain polysaccharides, allowing the sugars to enter the cell. The anti-sigma factor prevents a sigma factor from binding to DNA and increasing transcription of the associated PUL. Through a poorly characterized interaction with the STN (Secretin and TonB N-terminus) domain of the TBDT, the anti-sigma factor releases the sigma factor into the cytoplasm to bind to the PUL promoter. This experiment specifically attempted to purify six different anti-sigma factors in order to determine their structures. We began purifying two proteins encoded by genes BT4403 and BT4248, but both re- quire further study due to degradation between the two protein domains. Future research will address the degradation, as well as continue refining purification of these proteins in order to characterize their structure.

This project investigated the synthesis of tetrahydrocarbazoles formed via a Borsche-Drechsel cyclization. As a derivative of the widely studied indole moiety, tetrahydrocarbazoles have been shown to possess potent cytotoxic effects and biological activity for treatment against a variety of diseases. The method consists of a one pot synthesis of a substituted phenylhydrazine hydrochloride and a substituted cyclohexanone (Scheme 1) in the presence of antimony trioxide as a catalyst in methanol solvent at reflux temperatures. Products were isolated, purified and characterized by 1H NMR, 13C NMR, GC/MS, IR, elemental analysis and seven of nine of the derivatives were structurally characterized by X-ray crystallography.

Scheme 1. Tetrahydrocarbazoles investigated during URSI 2023.

Learned Categorical Perception–known as LCP–is the phenomenon where those who learn to categorize objects perceive or judge them differently. Objects in different categories may come to appear more distinct (“expansion”) and/or objects in the same category may come to appear more similar (“compression”).

Though LCP is often treated as firmly established, it does not always occur in experiments and it is unclear why. To determine when expansion and compression effects do and do not occur, we performed a meta-analysis on visual LCP research from 1994 until now. Our goal is to determine whether or not a strong effect exists overall and to analyze the study design choices that may contribute to stronger or weaker expansion and compression effects.

We searched the literature for relevant studies and after excluding those that were unusable for one reason or another, extracted the information necessary to calculate effect sizes in R. Both the exclusion and data extraction processes require a great deal of time and difficult decision-making and are not quitefinished, but preliminary results from analyses using the meta for R package suggest a moderate effect size for expansion and a weak effect size for compression. Further analyses will shed light on whether variables such as the specific LCP mea-ure used or aspects of the stimuli influence these effect sizes.

A funnel plot provides away to check for publication bias in the form of an absence of low-powered studies with low effect sizes despite many higher-powered studies with low effect sizes. The preliminary expansion graph shows significant asymmetry of this type, suggesting publication bias in the existing literature; thus the evidence for expansion effects may not be as strong as it seemed.

In an effort to promote transparent and scalable science, this summer we extended the functionality of jsPsych — an opensource library designed for researchers to run behavioral experiments online. We designed and implemented a new level of abstraction for jsPsych experiments, which allows users to share customizable experiment templates. Researchers can

use these templates to import different parts of each experiment and modify the experiments without building them from scratch. Our hope is that this will facilitate community-driven experiment development and easier reproducibility of different experiment designs.

To complement the template system, we developed the “Open Cognition Lab,” a mobile-first web app designed to host and run these experiments seamlessly. We plan to c reate shareable templates for many classic cognitive experiments and have interactive versions available on our app. Participants can then complete these experiments, testing their cognitive abilities from memory to imagery, and receive visualized feedback comparing their results to a global dataset. Upon completion, their data is, with their permission, added to the global dataset, which can then be downloaded by researchers. The app also supports classroom settings, where instructors can create groups with specified experiments for students to complete, fostering interactive learning experiences.

When studying aspects of human cognition such as attention or perception, knowing what someone is looking at in a given moment can be very informative. Many cognitive science experiments rely on this technique, often called gaze estimation or eye tracking. Researchers typically have to use expensive hardware to gather gaze data, limiting both the number of researchers with access to gaze estimation methods and the number of subjects that researchers can collect gaze data from ata time. An alternative to purpose-built laboratory hardware is to use off-the-shelf components, such as using computer vision techniques to estimate gaze location from webcam video. Webcam-based solutions enable research involving gaze estimation to be conducted remotely, widening the pool of participants for gaze-based research. This summer, we built an open-source webcam-based eye tracking software that uses deep learning to predict gaze location on a computer screen. We collected data from over five hundred participants for our training dataset. Our model uses embeddings to encode image features to remove unnecessary data, then uses an attention model to compare new images with calibration images by dynamically weighing the importance of data, and finally outputs predictions based on those comparisons. To maximize model accuracy, we conducted exploratory research to discover the optimal architecture and training configurations through hyperparameter tuning. Our future goal is to make implementation of this model simple through a browser-based web package containing the model, so that gaze estimation can be done on the web.

This summer, our URSI group’s task was to build and begin to implement the computing hardware and software for the second version of our lab’s humanoid robotics platform, Harper. The end goal for this project is to build vision and language systems that will enable the robot to be used in human-machine interaction experiments. To this end, we’re utilizing NVIDIA’s Jetson AGX Orin, an edge computing System on Chip (SoC) de- vice capable of performing 200 trillion operations per second. Because this system can implement relatively large artificial neural networks (ANNs) it functions as a central controller or nervous system for our robot. The robot body itself contains several sensory modules (which contain both co-processors and transducers for vision, hearing, and touch) capable of producing information that can be processed by software we’ve developed for the Jetson. One of these modules—the OAK-D Pro camera from Luxonis – mimics the human visual system using a pre-trained neural network (YoLo v4) embedded in the camera’s onboard processor. This module is immediately capable of recognizing and tagging the names of 80 common objects that it also locates, using a 3D coordinate frame, in the visual field. More objects can be learned with proper training, and a large language model (Nvidia’s RIVA) running on the Jetson will be integrated with visual information to allow coordination of speech, vision, and action by our chosen middleware suite (Robot Operating System, or ROS2). Work will continue on the project during the coming academic year.

Last year’s URSI project completed the construction of a humanoid robot, Harper, along with simple software for controlling its movements. Subsequent experiments with Harper revealed a number of weaknesses in the initial design, so this summer we set out to re-engineer the platform to address these issues.

(1) The size and mass of Harper made it intimidating in human-robot interaction (HRI) studies, so we set out to reduce the overall size by 15% in Harper 2.0. (2) The servo motors used in the initial build are difficult to control with precision. In addition, the worm gear system used in actuation was very inefficient and quickly suffers from uneven wear that produces unreliable movements and noisy actuation. We therefore set out to redesign the joints in the arms to use high quality stepper motors. This allows direct drive control for quieter, smoother operation and more precise movements at the shoulder. A hidden belt-pulley system for elbow movements accomplishes the same goals. (3) Although not completed this summer, several key components will be replaced by metal rather than 3D print- ed parts, and some printed components use new carbon-fiber materials for greater strength and resistance to wear. One result of these changes is a robot that is somewhat less similar to the human body in the details of its configuration, a consequence of shifting to a form-follows-function rather than function-fol- lows-form design philosophy. Further work this coming year will include efforts to sculpt body coverings that will restore greater similarity to the human form without compromising functionality.

Topic modeling is a type of statistical modeling that uses unsupervised machine learning to pull groups of similar words (topics) from a body of text. During this project, we explored how topic modeling can be used to study thematic variation in a large corpus of literature. While we compared multiple types of topic modeling, the two that stood out were Latent Dirichlet Allocation (LDA) and BERTopic. We chose LDA for its status as the preferred topic modeling method of the last two decades and its bag-of-words model, which contrasts with the newer BERTopic’s use of word sequence and semantic meaning through word embeddings. Previous research has been done with BERTopic on tweets and smaller texts,but we wanted to examine the performance on larger works, specifically entire books.

We constructed an LDA model using methods from pre-existing research, while down-weighting texts from the same author to increase topic coherence. This model served as a baseline to compare BERTopic against. Sinceless research has been conducted using BERTopicon larger texts, we experimented with a variety of parameters, filtering, and model types to increase topic quality. We narrowed our corpus to only fiction and developed a text-chunking process in order to improve topic coherence. Finally we estimated book publication dates to visualize and contextualize our findings temporally.

While LDA and similar bag-of-word models perform well on literature, while BERTopic may struggle for corpora that contain a wide range of styles and implicit themes.Our research provides a framework for processing larger texts to pass into BERTopic and advice on optimizing parameters. For future research with BERTopic on novels, the ability to adjust the correlation between topics and metadata, such as for authors like in our LDA model, may improve overall topic coherence and usefulness of models.

People of color, women, queer people, and people holding multiple of these identities have been and continue to be unwelcomed in STEM spaces. This summer we continued efforts at Vassar to redefine the dominant culture that has put up barriers for marginalized people in STEM by facilitating a sense of community and awe. To address this issue at Vassar we designed three new lab-basedexperiences in the Earth Science department. The first was “Open Mic’ Nights” which occurred every Monday evening from July 10th through 24th. This event brought together Vassar students, faculty, and Poughkeepsie community members within  Earth Science lab spaces. On these evenings, curated lab spaces in Ely were a site of curiosity and conversation between all the people who attended. The second, the Orientation Lab Demo, was part of the Foundation’s week from August 14th to August 19th. We welcomed first-year First-generation, Low Income (FLI) Program (formerly the Transitions Program) students who identify as people of color, low-income, and/or first-generation. These students typically do not have prior laboratory experiences to prepare them for the expectations at Vassar, and often feel differentiated from their peers. The purpose of the lab demo was to encourage under-repre- sented incoming students to explore what it means to have a positive first experience in a STEM setting. Lastly, we created the “Microscapes” exhibition opening September 27th. This event will be a culminating show for Open Mic’ Nightsand the Orientation Lab Demo that displays photographs taken by FLI students nd Open Mic’ Night guests over the course of the summer. The exhibit seeks to provide an accessible way for FLI students to plant their feet into the STEM world as well as provide a networking opportunity for them as firstyears.

This project was supported jointly by URSI and Grand Challenges.

A 9.82-m-long sediment core from Zipfeldberg Bog near Rhinebeck, New York was analyzed for organic matter, pollen, plant macrofossils, and charcoal to reconstruct vegetation and climate history since the retreat of the Laurentide ice sheet that covered our area 20,000 years ago. The Sphagnum (peat moss)-dominated bog overlies acid-buffering limestones, making its acidic pH unusual and suggesting that it might be a sensitive recorder of water level changes caused by climate. The site also contains several rare plant species, making a detailed history important for conservation. Preliminary results of the investigation reveal high percentages of boreal conifers near the base of the core, increases in alder and birch pollen during the Younger Dryastime period (12,900-11,500 years ago), and a nearly Holocene (last 10,000 years) peak in pine, followed by increases in deciduous species that signify the onset of warmth (e.g., oak). Sediments at the base of the core consist of clay and gyttja (organic muck), revealing a lake environment, with the earliest sediments radiocarbon dated at 14,256 +/- 315 ka. Oogo- nia (reproductive structures) of Chara (algae) are present in the gyttja, indicating an alkaline environment. Sphagnum rises in abundance at 6.3 m, coinciding with a decline in pine and a rise in beech and hickory pollen that we suggest occurred at ~8.5 ka based on pollen correlation to nearby records. A well-recognized mid-Holocene hemlock decline, which is tentatively dated to ~5.25 ka, coincides with more alkaline conditions, ev- idencedby the re-appearance of oogonia of Chara and declines in Sphagnum, and with less moisture, shown by the presence of sedge seeds. Despite the evidence for lower moisture, charcoal from forest fires is no more abundant during this period than prior to or after the hemlock decline. Subsequent increases in Sphagnum, commencing with hemlock recovery and continuing up to the present, indicate moisture increases in the late Holocene.

Momotombovolcano is in north-west Nicaragua, and Mon- te Galàn, a caldera, cuts into the north-western flank of the volcano. Recent lava flows from Momotombohave started to fill in the caldera, indicating the two have intertwined eruptive histories.

We characterized eruptive products from large eruptions to investigate if an overlap in plumbing exists. Plagioclase, orthopyroxene, and clinopyroxene crystals from tephra were mounted and polished to expose melt inclusions and prepare for analysis. We obtained geochemical measurements using Vassar’s Phenom scanning electron microscope (SEM) from melt inclusions, host crystals, and matrix glass. Melt inclusions form as magmas cool and minerals rapidly crystallize, trapping small amounts of melt. This glass reflects the composition of the magma at the time the crystal was forming, whereas matrix glass represents the composition at time of eruption.

Here, the weight percentage of SiO2 is used as a proxy for overall melt composition in glasses. SiO2 is the most abundant oxide in volcanic rocks and serves as the basis of their classification. Momotombo typically erupts lower SiO2 melts than those associated with the caldera. Based on the composition of matrix glass, we expect melt inclusions from Momotombo tohave <55 wt% SiO2 and Monte Galàn to have <70 wt% SiO2. Our data showed that SiO2 wt% in some melt inclusions from Momotombo is similar to the SiO2 wt% in the Monte Galán cal- dera inclusions. Many of our samples from Momotombo have crystals that contain inclusions with higher SiO2 than their matrix glass. The presence of these melt inclusions precludes us from ruling out a shared or common magma plumbing system. There is still much more research required to definitively prove that the two volcanic systems are interconnected, and these preliminary results will be furtherinvestigated over the coming academic year.

The Supplemental Nutrition Assistance Program (SNAP), also referred to as Food Stamps, provides financial assistance to over 40 million individuals in the United States in regards to their food purchases. While the program is federally funded, it is carried out by each state, who individually decide the disbursement methodology both in terms of ordering (i.e. by Case ID, Social Security number, etc.) and the number of disbursement dates within a calendar month. Each household receives all of their benefits once a calendar month on a single day. This singular-disbursement schedule perpetuates a phenomenon known as the SNAP Cycle: when a household depletes their SNAP payment early in the benefit month (the period between SNAP disbursements), they have less/lower-quality food later in the benefit month. With the arrival of next month’s benefits, the household once again spends their benefits quickly to counteract the food deprivation experienced at the end of the previous month. The SNAP Cycle has been found to have wide-reaching effects on outcomes such as food purchases and intake, test scores, drunk driving fatalities, quality of sleep, etc. This systematic review is the first to evaluate the literature pertaining to the SNAP Cycle and its various effects. In accordance with the PreferredReporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, two primary reviewers conducted an abstract review of papers sourced from three databases, PubMed, EconLit, and Scopus. Inclusion in a subsequent full-text review was determined based on pre-specified inclusion and exclusion criteria. The full-text review of 45 papers found that the SNAP Cycle had varying effects on eight identified outcome categories: purchases, food intake, behavior, health, performance, prices, finance, and econometric.

Though each outcome has its own trends, overall, the evidence suggests outcomes are impacted in response to the SNAP cycle.

We show that applying methods from optimal control theory to minimize the elastic energy of a slender elastic ribbon leads to constitutive equations that account for discontinuities in the curvature of the ribbon’s centerline. The Pontryagin Maximum Principle (PMP) provides a necessary condition for a ribbon configuration to be a local minimum of elastic energy, and we use the PMP to show that curvature discontinuities in the ribbon are analogous to switching controls in optimal control theory. We apply these methods to two elastic energy functionals for slender ribbons—the Sadowsky functional and a corrected Sadowsky function that was derived in previous work using gamma convergence. While all extremals of the Sadowsky functional are nonsingular, we find that the corrected Sadows- ky function admits extremals with singular arcs. After using the PMP to analyze discontinuities in the ribbon centerline, we perform a sensitivity analysis to compute the Jacobian matrix of boundary conditions at the final ribbon arc length with respect to boundary conditions at the initial arc length, with particular attention given to finding a transformation matrix that prop- agates the Jacobian across discontinuities. This matrix can be used to both detect bifurcations of equilibrium configurations as well as implement a shooting method to numerically compute ribbon configurations satisfying given boundary conditions. We then apply this numerical method to analyze four canonical problems involving elastic ribbons: helical ribbons and their stability, the behavior of discontinuities in spherical ribbons, the formation of Möbius bands, and buckling patterns in twisted ribbons.

A mathematical knot can be viewed as a piece of string that has been tied up and then has its ends fused together. We often view a knot as if it is resting on a table-top, where at most two strands cross over each other at any given point. The fewest number of crossings among all possible ways to lay the knot on the table is called the crossing number of the knot. The crossing number is a property that remains the same throughout continuous deformation, otherwise known as an invariant. Let’s take a look at another invariant. Imagine a loom with several strings on it. Any knot can be formed by tangling the strings on the loom and then connecting the ends. The braid index of the knot is the fewest number of strings needed on the loom to form the knot. Our project examined the statistical properties of the braid index of the set of two-bridge knots of a fixed c crossings.

We first discovered a closed formula for the number of two bridge knots of crossing number c and braid index b:

𝑒𝑒(𝑐𝑐, 𝑏𝑏) = 2^!"# )𝑐𝑐 − 𝑏𝑏+.

𝑏𝑏 − 2

From this formula we found the average braid index of a two-bridge knots with crossing number c as c goes to infinity:

𝑐𝑐 11

𝑎𝑎𝑎𝑎𝑒𝑒𝑎𝑎𝑎𝑎𝑎𝑎𝑒𝑒 = 3 + 9 .

We then used this average to find the variance as c goes to infinity:

𝑎𝑎𝑎𝑎𝑎𝑎𝑣𝑣𝑎𝑎𝑣𝑣𝑐𝑐𝑒𝑒 = 2𝑐𝑐 − 10

.

27 81

Finally, we proved what the median and mode braid index is for the set of two-bridge knots with crossing number c:

𝑐𝑐

𝑚𝑚𝑒𝑒𝑚𝑚𝑣𝑣𝑎𝑎𝑣𝑣 = 𝑚𝑚𝑚𝑚𝑚𝑚𝑒𝑒 = =

> + 1.

3

The basis of our findings is a method of turning two-bridge knots into “codes” which allows us to generate a comprehensive table of every two-bridge knot organized by crossing number and braid index. From this we found a recursive relationship that defined the number of codes for all two-bridge knots with a fixed crossing number c buta varying braid index b in terms of the sets of codes for two-bridge knots with smaller crossing number.

Mathematical epidemiology, one of the longest studied areas in mathematical biology, has significantly enhanced our understanding of how pathogens emerge, evolve, and spread within and between populations. We add to this body of work with a novel approach to modeling VisceralLeishmaniasis (VL) - a vector-borne, neglected tropical disease. Ours considers the role that climate change plays in the vulnerability of populations to VL. The vector responsible for the spread of VL, sandflies of the Phlebotomus and Lutzomyiagenera, develop dependent on environmental factors such as temperature and light duration. As climate change causes the average daily temperature to rise, sandflies’ diapause (overwinter dormant stage) gets shorter, making formerly inhospitable places suitable for sustained sandfly populations. Furthermore, warmer and wetter climates reduce the natural mortality of the sandfly through its egg, larva, and pupa life stages. This new climate regime may intro- duce sandflies to novel regions, and when coupled with their persistence in greater rnumbers in already established areas will increase the death toll of VL which stands at 10% with treatment up to 95% without. We compute basic reproductions thresholds for disease endemicity as well as an invasion threshold for the vectors introduced to novel regions. Coupling these analyses with numerical solutions of our mathematical model highlights the role climate change will have in causing otherwise avoidable mortality.

Although the universe contains over five times more dark matter than visible matter, constraining its non-gravitational interactions (if any) has been a challenge since its discovery. Historical evidence for dark matter (DM) comes from observing galaxy rotation curves, which imply that the mass of galaxies extends beyond their visible disks. We reproduce these historical measurements using a dataset from the SPARC collaboration and confirm that galaxy rotations cannot be explained without a DM component. In order to describe the behavior of dark matter, we construct a simple model of cosmological expansion and particle interaction which ultimately allows us to derive a form of the Boltzmann equation that tracks the number density of dark matter as the universe ages. We find that, while the universe is very young and dominated by radiation, dark matter eventually deviates from equilibrium and “freezes out” to a constant density in comoving coordinates. Freeze-out occurs when the temperature of the universe cools to the mass of the DM particle, which we assume here to be 100 GeV to correlate with proposed DM candidates called Weakly Interacting Massive Particles (WIMPs). In order to reproduce the observed DM relic density, this implies an electroweak-sized crosssection. Finally, we survey other interesting contemporary theories of dark matter that span the plane of masses and cross-sections.

Physics, astronomy, and other similar fields have acquired a reputation in mainstream circles as “objective” sciences, ostensibly detached from social inequalities as they study concepts above human interference. However, scientific studies and the lived experiences of marginalized physicists have confirmed the entrenchment of implicit bias in the discipline. Implicit bias is a cognitive process wherein a person’s unconscious social attitudes influence their perception or treatment of an out-group, such as people of color, LGBTQ+ people, women, and those that identify with countless other or multiple marginalized labels.

The motivation to address implicit bias in STEM at Vassar arose from a physics town hall meeting in the spring 2023 semester, where students voiced a desire for a workshop or similar training program. To that end, the main product of this research project is an hour-long workshop presentation planned for the early fall semester. It is informed by an extensive literature review but primarily discussion-based to keep participants en- gaged, while ensuring that attendees are participating at their comfort level and can leave or take breaks if needed. Discussion centers around three case studies, or hypothetical scenarios where implicit bias is inwardly or outwardly apparent. Participants will then be offered the chance to take an Implicit Association Test (IAT), the primary means of measuring bias levels against a specific group. Quantitative and qualitative data on the workshop’s effectiveness will be gathered through an anonymous feedback survey sent to participants’ emails. Our overall goal is a measurable increase in participants’ understanding of bias and an increase in their comfort levels addressing bias incidents.

This project was supported jointly by URSI and GrandChallenges.

Our URSI research explored the circumgalactic medium, CGM, through a 3-dimensional computer simulation of a Milky

Way-like galaxy. The CGM is the large cloud of hot diffuse gas that surrounds a galaxy and serves as the gas reservoir for star formation inside the galaxy itself; without the CGM there would be no ongoing star formation in the galaxy. We used a Python extension called The YT - Project which allowed us to visualize the data in three different ways. Slice Plots, ake a slice across a chosen axis for a variable such as density, temperature, or abundance of a selected element. Projection Plots, integrate across an axis for a chosen variable. Finally, PhasePlots take a weighted average of a variable or the total accumulation of a cell. Through these methods, we looked at the Faraday Effect, which is the phenomenon that causes polarization rotation of a beam of light due to a magnetic field, and specifically how magnetic fields interact with the CGM and contribute to galaxy formation.

We used ultrafast optics to refine our previous measurements for the speed of sound in Bismuth Tellurium Selenide (Bi- 2Te2Se) as well as measure phonon attenuation. Bi2Te2Seis a material that has many uses in electronic and nanoscale devices. However, it has become available so recently that very little research has been done on it. We used mechanical exfoliation to pick off pieces of a previously grown Bi2Te2Se crystal and stick them onto various types of wafers, seeing which ones would give us enough high quality crystals for us to be able to measure. We used a Titanium: Sapphire laser with a wavelength of 800nm on many crystals of different thicknesses, and measured the reflectivity vs. the time delay in picoseconds (10-12s). The laser’s pulses were less than a picosecond in duration with 13 nanoseconds in between and we split the pulses into two beams: pump and probe. A pump pulse hit the crystal first which produced sound waves that reverberated through the crystal, causing a change in the reflectivity of Bi2Te2Se. Soon after, a probe pulse arrived to measure said change. This process repeated itself millions of times each second. We measured the time delay between each successive spike in reflectivity to determine the speed of sound, as well as the phonon attenuation. From this we plan to study the elastic properties of Bi2Te2Se.

We are currently working on measuring larger crystals to measure the lifetime of phonons in Bi2Te2Se.

This project aimed to investigate the covariance in experimental variables involving the locomotion of C. elegans; specifically, identifying relationships between the variables and the Largest Lyapunov Exponent (LLE)associated with the locomotion of the worm. This study yields a better understanding if mean frequency and/or peak frequency are critical experimental parameters. In order to begin conducting the experiment to measure the covariance, the experimental setup facilitates the necessary measurement of a time series that contains information about the locomotory complexity as well as thrashing frequencies. The C. elegans is exposed to a HeNe Laser in a water column generating a diffraction pattern that is recorded by a photodiode. We observed no covariance between swimming frequencies and LLEs indicating that the complexity of the locomotion is independent of swimming rates

Previous diffraction studies of the locomotion of C.elegans found the Largest Lyapunov exponent (LLE)to be positive indicating the presence of chaos in the system. The definition of a hyperchaotic system is one with at least two positive LLEs. We investigate the possibility of hyperchaos in the locomotion of the nematodes using Lyapunov spectra. The estimated spectra are calculated using the Eckmann-Ruelle algorithm, a Jacobian-based method for calculating the spectra of experimental time series. Preliminary results show the presence of two positive exponents. Comparing the estimates with the LLE obtained from the Rosenstein algorithm indicates that one of the two might be spurious, which means that it’s a byproduct of the algorithm and the system would not be hyperchaotic.

In future work, we will examine hyperchaos using different methods - such as time inversion - which will filter out the spurious Lyapunov Exponents from estimated spectra.

A topological insulator is a material that supports unidirectional currents regardless of imperfections in its lattice. In recent years, topological phases have been demonstrated in classical systems. In this work, we present the development of a technique based on electron beam lithography (EBL) for the micro-fabrication of mechanical and plasmonic topological insulators. Among the most important results are the fabrication of topological arrays of aluminum lines and circles with a maximum resolution of 200 nanometers. To create these structures, we perform EBL using a scanning electron microscope (SEM) on silicon or indium tin oxide substrates. It is important to note that this groundbreaking process utilizes an SEM that is intended solely for imaging purposes. Our method has been demonstrated to be an accessible tool for undergraduate students and opens an important venue to provide experience on this state-of-the-art fabrication technique that can be too expensive or inaccessible for many.

Locomotion

The nematode Caenorhabditis elegans (C. elegans) has a comparatively simple neurological system consisting of 302 neurons, which makes it a useful model organism. Previous work has found the locomotion of C. elegans displays markers of chaos, including a positive largest Lyapunov exponent (LLE).In this investigation, locomotory time series from wildtype C. elegans using optical diffraction techniques was analyzed to try to better understand one chaotic marker of the system known as Kolmogorov-Sinai (KS) entropy. The relation KS entropy shares with the positive Lyapunov spectrum of a dynamical system, in conjunction with its usage as a potential chaotic marker itself, motivates the computation of this value for our system. To calculate the KS entropy, Faure and Lesne’s method (2015) is applied, where statistics from recurrence quantification analysis (RQA)of recurrence plots are gathered to determine the distributions of recurrences across the phase space of each time series. Recurrence distribution information will then be used to compute the value of the KS entropy. In future work, we hope to link the calculated value of KS entropy to the LLE of the system as well as the RQA divergence through a series of known relations. Preliminary results for the RQA divergence reveal three distinct value regions: ~ 0.036 s-1, ~ 0.068 s-1, and ~ 0.166 s-1.

Fear generalization involves the ability to transfer a learned response from one stimulus to a related, but not identical, other stimulus. Generalization is balanced with the ability to discriminate between analogous stimuli to limit response overexpression. The infralimbic cortex (IL) playa role in fear memory modulation, most notably in extinction. While there is some evidence linking IL functionality with fear memory generalization, the exact role for the IL in cued fear memory generalization is unknown. This study utilizes the chemogenetic technique DREADDs (Designer Receptors Exclusively Activated by DesignerDrugs) to inhibitor excite IL pyramidal neuron activity during the expression of cued fear memory generalization. To verify the efficacy of the inhibitory (Gi) and excitatory (Gq) DREADD, we utilize dc-fos immunohistochemistry to indicate neuronal activity. We hypothesized that stimulation of IL neurons would promote memory discrimination while inhibition of IL neurons would promote memory generalization. In ongoing research, we are determining whetheractivation of the dorsal peduncular cortex (DP), a brain area that is located ventral to the IL, alters memory generalization as we observed virus transfection spanning into the DP. The activation of the DP is involved in stress and anxiety-like behavior(Botterill et. al, 2023), so virus transfection in the DP has important implications in our research.

In nature, danger is pervasive, necessitating an ability to predict and respond o a wide variety of perilous situations. Generalization acts as one solution, where the individual utilizes knowledge of a stimulus previously associated with danger to respond in the same way to a similar stimulus.While often beneficial for survival, excessive generalization (overgeneralization) can be maladaptive, and may contribute to clinical disorders such as anxiety and post-traumatic stress disorder (PTSD). In previous experiments, we discovered a high degree of variability in the generalization of fear conditioning. How individual differences in generalization correlate with extinction and unconditioned anxiety-like behaviors remains unknown. Here, we ran ArcCreERT2 x eYFP mice on a battery of behavioral tasks, including the novel open field, elevated zero maze, auditor-cued fear conditioning, generalization, and extinction. After grouping mice into high or low “generalizers” using a K-means clustering algorithm, an analysis on extinction revealed that male high generalizers showed an extinction performance deficit (difficulty learning that a stimulus is no longer dangerous). Female high and low generalizers showed no differences in extinction performance. Generalization performance also correlated with several anxiety-like behaviors in the novel open field and elevated zero maze. Interestingly, anxiety-like behavior was not predicted by fear conditioning or extinction performance. This indicates that generalization is a unique predictor of both extinction performance and anxiety-like behavior. These results indicate important sex differences in associative fear conditioning as well as uncovering a possible novel phenotype for modeling individual variability in fear learning that may be related to anxiety disorders and PTSD. Future directions include exploring possible overlap in neuronal ensembles underlying fear memory generalization and extinction.

Astrocytes arecells in the brain that modify blood flow, energy production, cell to cell communication, and are an integral component in an immune response to protect tissue. The immune response can be observed through increases in glial fibrillary acidic protein (GFAP) within astrocytes. These functions can influence synaptic plasticity, a critical component of memory. Our study focuses on the relationship between astrocytic activity and spatial working memory. We employed a chemogenetic technique (Designer Receptors Exclusively Activated by Designer Drugs, DREADDs) to activate astrocytes through intracellular calcium increases in the prelimbic cortex or dorsal hippocampus of male and female Long Evans rats during a delayed spontaneous alternation task. Bilateral injections of a DREADDs virus, either pAAV-GFAP-hM3D(Gq)- mCherry or (PHP.eB)-GfaABC1D-DREADD hM3D-mCherry- 4x6T-CW3SL, or a control virus, pAAV.GFAP.eGFP.WPRE.hGH (serotype 5)or PHP.eB-GfaABC1D-smV5-4x6T were given. After two weeks to allow for cells to develop receptors, rats underwent delayed spontaneous alternation testing in which they received intraperitoneal injections of either the corresponding designer drug (hM3D(Gq) receptor agonist), compound 21 (C21) or saline 30 minutes before delayed spontaneous alternation testing in a counterbalanced order at least 48 hrs apart. Visual cues were changed to provide novel stimuli for each testing session. DREADDs activation with C21 led to impairments on spatial working memory in females while males did not show impairments. GFAP increased in cells with DREADDs receptors and this effect was greater in females compared to male rats, potentially suggesting activating astrocytes through DREADDs might lead to an astrocytic immune response. Our research indicates astrocytes play an integral role in memory processes in the prefrontal cortex and hippocampus and are a novel target for treatment in neurodegenerative diseases.

medium-chainInsulin resistance increases with age, leading to increases in blood glucose, particularly after carbohydrate consumption. This dysregulation of blood glucose can lead to increased cogntive impairments. The ketogenic diet is nutritionally complete and consists of medium chain triglycerides, reducing the need for insulin and potentially enhancing cognitive functioning across the lifespan. Astrocytes in particular have been shown toplay important roles in controlling blood flow through neurovascular coupling, processing glucose, and storing and breaking down glycogen during learning and memory. These astrocytic processes can be disrupted by aging and neurodegenerative diseases. Our study examine sastrocytic proteins to determine if changes with age can be mitigated by ketogenic diets. Young adult (6 months)and aged (24 months) male and female F344 x Brown Norway F1 hybrid rats were assigned a time-restricted ketogenic MCT-enriched diet (76% MCT oil; TRF-KMCT), a time/calorie-matched control diet (65% carbohydrates; TRF-CARB), or ad libitum(AL) access to standard chow (65% carbohydrates; AL-CHOW) for 8 weeks. Glutamine synthetase, an astrocyte-specific enzyme involved in glutamate and GABA recycling, and glial fibrillary acidic protein (GFAP), a structural protein that increases with inflammation, were examined in the perirhinal cortex (PRh), posterior agranular insular cortex (AIP), and caudate putamen (CPu). Previous studies indicate the PRh and AIP can show a decline with age, while CPu shows relatively better maintenance of function and size. When examining glutamine synthetase expression, females showed increased staining with age in the cortical areas, while males did not. Preliminary results suggest sex differences in GFAP expression with age as well. These results open the door for more exploration into changes in astrocyte function with age, and the potential role of ketogenic diet in reducing the glucose dysregulation that leads to cognitive impairment.

Appetitive operant conditioning often uses food or water to reward correct responses, but motivation for the reward requires food or water restriction, necessitating vigilant monitoring and high USDA classification for pain and distress. Our lab studies the role of astrocytes in cognition using appetitive behavioral tasks. Recent studies have used unrestricted citric acid water to motivate behavior for a non-citric acid water reward. This is important when studying astrocytes, which are involved in glucose metabolism and water regulation in aquaporin channels. Our study examines if ad libitum 2% citric acid water will motivate behavior for a non-citric acid water reward on a difficult-to-learn sustained attention task. Male and female Long Evans rats were trained on a sustained attention task in which trials are presented at variable intervals(12+/-3 s) and rats must respond to a light signal (25, 100, or 500 ms) by pressing one lever for a signal and another for a nonsignal. There is no significant difference in time to learn the task, indicating sufficient motivation from the less palatable citric acid water as compared to water restriction. Rats given citric acid water had slightly higher average weights, indicating that using citric acid may mitigate the weight loss problem of water restriction. To assess functional changes in astrocytes, we used immunohistochemistry to stain for glutamine synthetase, a marker of astrocytic activity in recycling of glutamate and GABA, the major excitatory and inhibitory neurotransmitters. Staining data showed no significant difference in the area that astrocytes cover in brain regions of interest but does show significantly higher density and darker staining in the citric acid brains, an effect we will be exploring as we continue the project. Overall, our results suggest that citric acid water may provide a viable alternative to water restriction for appetitive operant conditioning on cognition tasks.

Astrocytes are essential for recycling of glutamate and GABA, the primary excitatory and inhibitory neurotransmitters in the central nervous system. Astrocytes have the enzyme glutamine synthetase (GS) that neurons lack, which allows them to turn excess glutamate to glutamine that is then given back to the neuron and can be turned back to glutamate or GABA in the neuron. This process is known as the glutamate-glutamine cycle. Methionine sulfoximine (MSO) is a selective GS inhibitor that allows us to study the role of GS in spatial working memory. Male and female Long Evans rats were surgically implanted with bilateral guide cannulae into their prefrontal cortex or hippocampus. Fifteen minutes prior to behavioral testing, rats were intracranially microinjected through the guide cannulae with either saline, 0.4mM MSO, 2mMMSO, or10mM MSO on a pseudo-randomized schedule, allowing at least 48 hours between injections for the effects of MSO to wear off. Spatial working memory behavior was tested on a 20-minute four arm maze task, recording a success n alternation as an entry into all four arms of the maze within a set of five arm entries. Following all behavioral testing, rats were perfused and brains were Nissl stained to check for cannulae placement. Preliminary results seem to suggest that lower concentrations of MSO (0.4mM) improve spatial working memory, but higher concentrations (2mM or 10mM MSO) lead to cognitive deficits.

Racial colorblindness refers to the belief that individuals should be treated as equally as possible, without regard to race. In Study 1 we investigated whether people who prescribe to colorblind ideology cognitively process information about race in a fundamentally different manner than those who take a more race-conscious approach. Results indicated individuals who claim to “not see race” perform similarly as their race-conscious peers on a racial memory recall task, with a tendency to overestimate the number of White faces in a given scene. In recent years, colorblind ideology has gained mainstream recognition and was cited in the recent Supreme Court ruling reversing a half decade of affirmative action in college admissions.

This ruling was heralded as a step toward a more colorblind society where students are evaluated through ability, not race. However, existing literature suggests individuals who endorse racial colorblindness may perpetuate existing racial inequalities by ignoring the need for targeted policies that acknowledge historical and social contexts. Study 2 had participants take on the role of admissions office rat an elite university and evaluate an applicants’ qualifications to make recommendations to the university. Our findings show students of color were rated as less qualified and were less likely to be recommended for admission when the university explicitly mentioned the Supreme Court ruling compared to a control condition. Additionally, applicants who mentioned their racial minority background in their personal essay received lower evaluations and were less likely to be recommended for admission compared to applicants of color who did not mention their race. This effect was pronounced among participants who strongly endorsed racial colorblindness. Moreover, participants expressed negative evaluations of legacy admissions and were less likely to recommend legacy students for admission compared to non-legacy students.

This project was supported jointly by URSI and GrandChallenges.

Meritocratic ideology is firmly woven into the fabric of American society. In education, meritocratic principles are promoted as a fair method of evaluating students’ performance and accomplishments, suggesting students are given equal opportunities to succeed regardless of their background; however, prior research has shown otherwise. Lower socioeconomic status (SES) has been linked to lower academic achievement and delayed academic progress. Three studies examined various markers of socioeconomic status and their influence on the attributions, predictions and recommendations made about student performance and potential. Study 1 found individuals strongly endorsing meritocracy credited poor student performance to internal attributions such as work ethic and talent regardless of their school resources. In Study 2, participants acknowledged the role of external factors in the attributions they made for high-performing students attending an over-resourced school compared to an under-resourced school. Study 3 demonstrates perceivers are aware of SES-based opportunity gaps as evidenced by participants’ increased likelihood of attributing student success to home life and family resources when viewing a student from a high SES background. However, awareness of these inequities only served to benefit wealthy students, as they were more likely to be recommended for admission into a selective high school compared to students from the lowest rung of the socioeconomic ladder. Additionally (and ironically) belief in meritocracy reinforced SES-based outcome disparities as those who strongly endorsed meritocratic beliefs were most likely to favor students coming from wealthy backgrounds compared to students from poor backgrounds, despite equal academic achievements. Taken together, participants recognize the challenges faced by students from low SES backgrounds but these challenges do not significantly influence recommendation decisions nor attributions for student performance.

This project was supported jointly by URSI and Grand Challenges.

Several studies of resilience have cited the positive effects of the ability to thrive despite experiences of personal and social stress across the lifespan, and incorporating protective measures, such as mindfulness meditation, into one’s routine to buffer against adverse effects of stress and build resilience. Mindfulness health-related benefits include enhanced emotional processing and improved self-efficacy and control, which can be linked to greater moment-to-moment, nonjudgmental awareness (Kabat-Zinn, 1994). The present study aims to develop a new protocol for studying the potential influence of mindfulness techniques in buffering against cognitive impairments due to stress experienced by young adults, such as emotional distress, lack of sleep, or fatigue, by validating the usage of new technology used to evaluate neural health to draw potential links of cognitive attention to resilience in college students.

Moreover, as studies suggest that mindfulness ability and positive benefits arise gradually over time (Kabat-Zinn, 2015), the present study design aims to bolster the effectiveness of single mindfulness interventions and the improvement of behavioral motivation by including instruction on the benefits of mindfulness in the context of self-compassion (Neff,2003) and developing a growth mindset (Burnette et al, 2020) on cognitive attention. Exploring potential protective measures to promote resilience in young adults can provide a greater understanding of the development of resilience and the promotion of greater well-being throughout the lifespan.

Dopamine (DA) neurons play an important role in mediating social behavior. During social interaction there is an increase in activity of DA neurons in the ventral tegmental area (VTA). Inhibition of these neurons leads to reduced sociability whereas increasing their activity promotes sociability. Our lab is interested in measuring DA neuron activity in real time during social interactions, and we’ve established a microendoscopy-based approach which relies on calcium-dependent fluorescence as an indicator of cell activity. Unfortunately, image resolution is suboptimal and has made individual-cell level activity visualization impossible. The aim of this URSI project is to optimize our procedure to improve the quality of neural activity data obtained. We focused on two aspects of the previous procedures: adjusting the surgical protocol and using a transgenic mouse with a potentially more specific pattern of expression of the cal- cium-dependent reporter, GCaMP. We found that modification of the surgical protocol did not increase our ability to visualize activity of DA neurons in the VTA. However, use of the transgenic mouse line improved neural signal detection, although we have not yet determined if the improvement is sufficient for cell-specific activity measurements.

Voluntary exercise contributes to stress resiliency by decreasing activation of the hypothalamic-pituitary-adrenal (HPA) axis, the pathway that regulates the hormonal response to stress.

Reduced HPA axis activation in turn attenuates release of stress-induced corticosterone. In a recent study, the Zupan lab has found that postpartum maternalexercise is correlated with increased stress resilience in adult offspring, suggesting that voluntary exercise may have intergenerational effects on stress resiliency. Voluntary exercise has been shown to enhance maternal care in rats and mice, leading to decreased anxiety-type behavior in adult offspring. Our URSI project aims to determine if maternal access to voluntary exercise causes this stress resiliency. We also aim to assess whether changes in maternal behavior are associated with the observed intergenerational benefit of exercise. We tested 16 litters of mice, 8 of which had dams with running-wheel access, 8 of which did not. We cross-fostered half of the pups in each litter to a different dam to test whether different postnatal environments increased stress resiliency in adulthood. We also looked at maternal care, assessing dam time on nest, licking/grooming, and archedback nursing over the 3-week period of postnatal care. Adult offspring were then tested for anxiety-like behavior and stress responsivity, measured by blood corticosterone measurements and weight changes following an acute stressor. We found no differences in litter size and pup weight between our groups and we observed comparable levels of maternal care between runner and sedentary dams, indicating that running wheel access had no effect on gross development of pups and dam maternal behavior. Analysis of adult offspring behavioral and stress data is ongoing.

The mesocorticolimbic (MCL) dopamine (DA) circuit is comprised of cells that originate in the ventral tegmental area (VTA) and project to various brain regions, including the prefrontal cortex, nucleus accumbent (NAc) and amygdala. Activity of DA neurons projecting to the NAc mediates natural rewards like food and social interaction. Increasing the activity of these neurons increases conspecific social interaction while suppression of the same neurons leads to reduced sociability. The MCL circuit has been implicated in dysregulated social behavior in human social disorders. The Fmr1-deficient mouse, a model of Fragile X Syndrome and the largest single-gene cause of autism spectrum disorder, exhibits dysregulated social behavior. The Zupan lab has previously reported that Fmr1-deficient mice are hypersocial, but there could be several reasons for this dysfunction including a deficit in social cue perception and/or a dysregulated reward pathway. My URSI project aims to answer if the social dysfunction in Fmr1 deficient mice is associated with dysregulated reward circuitry. Using an operant conditioning task, we asked 46 female mice to perform work, specifically lever presses, in order to obtain access to a social conspecific. If social interaction is rewarding, the mouse will perform work to obtain the positive reinforcer. We quantify“how” rewarding the interaction is by the amount of work the mice are willing to do. Preliminary data analysis shows that Fmr1-deficient mice are more likely to acquire the task and press a lever for a social reward, suggesting that they are more motivated by the social reinforcer than controls. Mice that acquired the task, however, showed no differences in the “value” of the reinforcer. Importantly, we found no differences in acquisition or performance of the task when the reinforcer was sugar water, indicating that the difference in reward perception is specific to the social modality.